9-91090533-G-T

Variant names:

• chr9-91090533-G-T
• rs430794
• ENST00000663149.1:n.966+7889C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_184105.1(LINC02937):​n.2294+7889C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,032 control chromosomes in the GnomAD database, including 10,621 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.36 (10621 hom., cov: 32)
• Consequence: LINC02937 NR_184105.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53
• Publications: 15 publications found

Genes affected

LINC02937 (HGNC:55942): (long intergenic non-protein coding RNA 2937)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_184105.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02937	NR_184105.1		n.2294+7889C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02937	ENST00000663149.1		n.966+7889C>A		intron	N/A
	LINC02937	ENST00000666264.1		n.463-621C>A		intron	N/A
	LINC02937	ENST00000686463.2		n.401+7889C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55295 AN: 151914 Hom.: 10619 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.381

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.364 AC: 55336 AN: 152032 Hom.: 10621 Cov.: 32 AF XY: 0.366 AC XY: 27176 AN XY: 74312

African (AFR) AF: 0.468 AC: 19423 AN: 41468

American (AMR) AF: 0.350 AC: 5341 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1532 AN: 3470

East Asian (EAS) AF: 0.487 AC: 2515 AN: 5160

South Asian (SAS) AF: 0.463 AC: 2229 AN: 4818

European-Finnish (FIN) AF: 0.303 AC: 3201 AN: 10574

Middle Eastern (MID) AF: 0.418 AC: 122 AN: 292

European-Non Finnish (NFE) AF: 0.294 AC: 19951 AN: 67966

Other (OTH) AF: 0.380 AC: 801 AN: 2106

Alfa AF: 0.317 Hom.: 8838

Bravo AF: 0.373

Asia WGS AF: 0.500 AC: 1737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.15
DANN	Benign	0.52
PhyloP100		-2.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs430794; hg19: chr9-93852815;